From 45a832c4ff08f531475a60c8b6a6a4c08d083c4f Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 23 Oct 2024 09:30:20 +0200
Subject: [PATCH 01/56] Bump dependencies for NumPy 2 compatibility

---
 pyproject.toml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 09fbdad9..cb00931b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,11 +8,11 @@ description = "The WFDB Python package: tools for reading, writing, and processi
 authors = [{name = "The Laboratory for Computational Physiology", email = "contact@physionet.org"}]
 license = {text = "MIT License"}
 readme = "README.md"
-requires-python = ">= 3.8"
+requires-python = ">= 3.9"
 dependencies = [
-    "numpy >= 1.10.1, < 2.0.0",
+    "numpy >= 1.26.4",
     "scipy >= 1.0.0",
-    "pandas >= 1.3.0",
+    "pandas >= 2.2.0",
     "soundfile >= 0.10.0",
     "matplotlib >= 3.2.2",
     "requests >= 2.8.1",
@@ -35,7 +35,7 @@ documentation = "https://wfdb.readthedocs.io/"
 
 [tool.black]
 line-length = 80
-target-version = ['py37']
+target-version = ["py39"]
 
 [tool.hatch.build.targets.sdist]
 exclude = [

From 53047e22dee04e498976fedff8529c6cbb515355 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 23 Oct 2024 09:49:15 +0200
Subject: [PATCH 02/56] Fix CI

---
 .github/workflows/run-tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index dc0d322e..6b9f44c9 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -17,7 +17,7 @@ jobs:
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
       - name: Setup uv

From 3105f32a65600138e33dfd9e4dc9114f36d6c269 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 23 Oct 2024 09:51:08 +0200
Subject: [PATCH 03/56] Bump scipy for Python 3.13

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index cb00931b..b28c73f3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,7 @@ readme = "README.md"
 requires-python = ">= 3.9"
 dependencies = [
     "numpy >= 1.26.4",
-    "scipy >= 1.0.0",
+    "scipy >= 1.14.1",
     "pandas >= 2.2.0",
     "soundfile >= 0.10.0",
     "matplotlib >= 3.2.2",

From 6bd08fb0a7804d77a29828f1e5a0c29f4b6ab530 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Wed, 23 Oct 2024 09:53:11 +0200
Subject: [PATCH 04/56] Bump Python to 3.10

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b28c73f3..4c8d56f1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ description = "The WFDB Python package: tools for reading, writing, and processi
 authors = [{name = "The Laboratory for Computational Physiology", email = "contact@physionet.org"}]
 license = {text = "MIT License"}
 readme = "README.md"
-requires-python = ">= 3.9"
+requires-python = ">= 3.10"
 dependencies = [
     "numpy >= 1.26.4",
     "scipy >= 1.14.1",

From f1f1ab932da7bbed91bd3806b61ac59215597f71 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Fri, 25 Oct 2024 10:23:34 +0200
Subject: [PATCH 05/56] Include Python 3.9 again

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4c8d56f1..b28c73f3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ description = "The WFDB Python package: tools for reading, writing, and processi
 authors = [{name = "The Laboratory for Computational Physiology", email = "contact@physionet.org"}]
 license = {text = "MIT License"}
 readme = "README.md"
-requires-python = ">= 3.10"
+requires-python = ">= 3.9"
 dependencies = [
     "numpy >= 1.26.4",
     "scipy >= 1.14.1",

From 3445bef8d350201a3f3042f6f4331a9dfba7adb9 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Mon, 18 Nov 2024 13:31:09 +0100
Subject: [PATCH 06/56] Try to replace uv run

---
 .github/workflows/run-tests.yml | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index 6b9f44c9..873d6e86 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -23,15 +23,19 @@ jobs:
       - name: Setup uv
         uses: astral-sh/setup-uv@v3
       - name: Install Python ${{ matrix.python-version }}
-        run: uv python install ${{ matrix.python-version }}
+        run: |
+          uv python install ${{ matrix.python-version }}
+          uv venv
+          uv pip install -e ".[dev]"
+          source .venv/bin/activate
       - name: Install libsndfile
         if: startsWith(matrix.os, 'ubuntu')
         run: |
           sudo apt-get install -y libsndfile1
       - name: Run tests
-        run: uv run --extra dev pytest
+        run: pytest
       - name: Check source code format
-        run: uv run --extra dev black --check --diff .
+        run: black --check --diff .
 
   test-deb10-i386:
     runs-on: ubuntu-latest

From e2ff829aa4c9fc65cc9da335d7c2959b5c890bf2 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Mon, 18 Nov 2024 13:34:18 +0100
Subject: [PATCH 07/56] Downgrade scipy

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b28c73f3..14080e5c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,7 @@ readme = "README.md"
 requires-python = ">= 3.9"
 dependencies = [
     "numpy >= 1.26.4",
-    "scipy >= 1.14.1",
+    "scipy >= 1.13.0",
     "pandas >= 2.2.0",
     "soundfile >= 0.10.0",
     "matplotlib >= 3.2.2",

From 4b3e4c6dbbc352d53b2a5db2e6d96d8713939e4c Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Mon, 18 Nov 2024 13:36:02 +0100
Subject: [PATCH 08/56] Run as module

---
 .github/workflows/run-tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index 873d6e86..8e6b4944 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -33,9 +33,9 @@ jobs:
         run: |
           sudo apt-get install -y libsndfile1
       - name: Run tests
-        run: pytest
+        run: python -m pytest
       - name: Check source code format
-        run: black --check --diff .
+        run: python -m black --check --diff .
 
   test-deb10-i386:
     runs-on: ubuntu-latest

From 7cffcda9a8f4226e5a8a8ecdbed6042b4a9e5dcb Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Mon, 18 Nov 2024 13:38:57 +0100
Subject: [PATCH 09/56] Back to uv run

---
 .github/workflows/run-tests.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index 8e6b4944..9dc161b0 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -27,15 +27,14 @@ jobs:
           uv python install ${{ matrix.python-version }}
           uv venv
           uv pip install -e ".[dev]"
-          source .venv/bin/activate
       - name: Install libsndfile
         if: startsWith(matrix.os, 'ubuntu')
         run: |
           sudo apt-get install -y libsndfile1
       - name: Run tests
-        run: python -m pytest
+        run: uv run pytest
       - name: Check source code format
-        run: python -m black --check --diff .
+        run: uv run black --check --diff .
 
   test-deb10-i386:
     runs-on: ubuntu-latest

From 7dd56174fa95ee76a8676a20aec84633f4223983 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Mon, 18 Nov 2024 13:41:36 +0100
Subject: [PATCH 10/56] Use --system option

---
 .github/workflows/run-tests.yml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index 9dc161b0..e683a80c 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -10,7 +10,9 @@ on:
     branches:
       - main
 
-# Set the language, install dependencies, and run the tests
+env:
+  UV_SYSTEM_PYTHON: 1
+
 jobs:
   build:
     runs-on: ${{ matrix.os }}
@@ -25,16 +27,15 @@ jobs:
       - name: Install Python ${{ matrix.python-version }}
         run: |
           uv python install ${{ matrix.python-version }}
-          uv venv
           uv pip install -e ".[dev]"
       - name: Install libsndfile
         if: startsWith(matrix.os, 'ubuntu')
         run: |
           sudo apt-get install -y libsndfile1
       - name: Run tests
-        run: uv run pytest
+        run: pytest
       - name: Check source code format
-        run: uv run black --check --diff .
+        run: black --check --diff .
 
   test-deb10-i386:
     runs-on: ubuntu-latest

From 52dd99b9cb504415933c866040081ec6340263da Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Mon, 18 Nov 2024 13:45:52 +0100
Subject: [PATCH 11/56] Revert

---
 .github/workflows/run-tests.yml | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index e683a80c..309baaf8 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -10,9 +10,6 @@ on:
     branches:
       - main
 
-env:
-  UV_SYSTEM_PYTHON: 1
-
 jobs:
   build:
     runs-on: ${{ matrix.os }}
@@ -25,17 +22,15 @@ jobs:
       - name: Setup uv
         uses: astral-sh/setup-uv@v3
       - name: Install Python ${{ matrix.python-version }}
-        run: |
-          uv python install ${{ matrix.python-version }}
-          uv pip install -e ".[dev]"
+        run: uv python install ${{ matrix.python-version }}
       - name: Install libsndfile
         if: startsWith(matrix.os, 'ubuntu')
         run: |
           sudo apt-get install -y libsndfile1
       - name: Run tests
-        run: pytest
+        run: uv run pytest
       - name: Check source code format
-        run: black --check --diff .
+        run: uv run black --check --diff .
 
   test-deb10-i386:
     runs-on: ubuntu-latest

From 1f3bacd8fd817a52d907438a2b38415753012cd4 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Mon, 18 Nov 2024 13:50:34 +0100
Subject: [PATCH 12/56] Sync

---
 .github/workflows/run-tests.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index 309baaf8..b8e47eb5 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -27,6 +27,8 @@ jobs:
         if: startsWith(matrix.os, 'ubuntu')
         run: |
           sudo apt-get install -y libsndfile1
+      - name: Install dependencies
+        run: uv sync --all-extras
       - name: Run tests
         run: uv run pytest
       - name: Check source code format

From 7fb608e664acf223140da2b28832efc47fc34ba0 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Mon, 18 Nov 2024 15:42:42 +0100
Subject: [PATCH 13/56] Try forking

---
 pyproject.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 14080e5c..86ecf1cf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,8 @@ readme = "README.md"
 requires-python = ">= 3.9"
 dependencies = [
     "numpy >= 1.26.4",
-    "scipy >= 1.13.0",
+    "scipy >= 1.13.0; python_version >= '3.9'",
+    "scipy >= 1.14.0; python_version >= '3.10'",
     "pandas >= 2.2.0",
     "soundfile >= 0.10.0",
     "matplotlib >= 3.2.2",

From b2ffd5179ddbfb57455a5b0e8c179ed409aae5a1 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 19 Nov 2024 08:05:37 +0100
Subject: [PATCH 14/56] Try >= 3.10

---
 .readthedocs.yml | 2 +-
 pyproject.toml   | 7 +++----
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 9fedd977..7d45d867 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -5,7 +5,7 @@ version: 2
 build:
   os: "ubuntu-20.04"
   tools:
-    python: "3.9"
+    python: "3.10"
 
 # Build from the docs/ directory with Sphinx
 sphinx:
diff --git a/pyproject.toml b/pyproject.toml
index 86ecf1cf..96aaf5a6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,11 +8,10 @@ description = "The WFDB Python package: tools for reading, writing, and processi
 authors = [{name = "The Laboratory for Computational Physiology", email = "contact@physionet.org"}]
 license = {text = "MIT License"}
 readme = "README.md"
-requires-python = ">= 3.9"
+requires-python = ">= 3.10"
 dependencies = [
     "numpy >= 1.26.4",
-    "scipy >= 1.13.0; python_version >= '3.9'",
-    "scipy >= 1.14.0; python_version >= '3.10'",
+    "scipy >= 1.14.0",
     "pandas >= 2.2.0",
     "soundfile >= 0.10.0",
     "matplotlib >= 3.2.2",
@@ -36,7 +35,7 @@ documentation = "https://wfdb.readthedocs.io/"
 
 [tool.black]
 line-length = 80
-target-version = ["py39"]
+target-version = ["py310"]
 
 [tool.hatch.build.targets.sdist]
 exclude = [

From 2349a410ac15197a02f868cd24b88d4d5ea29ce9 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 19 Nov 2024 08:57:09 +0100
Subject: [PATCH 15/56] Try with setup-python action

---
 .github/workflows/run-tests.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index b8e47eb5..e50f3dae 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -19,10 +19,10 @@ jobs:
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
-      - name: Setup uv
-        uses: astral-sh/setup-uv@v3
-      - name: Install Python ${{ matrix.python-version }}
-        run: uv python install ${{ matrix.python-version }}
+      - uses: astral-sh/setup-uv@v3
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
       - name: Install libsndfile
         if: startsWith(matrix.os, 'ubuntu')
         run: |

From 7c3daabce49cf89e738baa260978c17b0be6e65c Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 19 Nov 2024 09:12:24 +0100
Subject: [PATCH 16/56] Revert "Try with setup-python action"

This reverts commit 2349a410ac15197a02f868cd24b88d4d5ea29ce9.
---
 .github/workflows/run-tests.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index e50f3dae..b8e47eb5 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -19,10 +19,10 @@ jobs:
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
-      - uses: astral-sh/setup-uv@v3
-      - uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v3
+      - name: Install Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
       - name: Install libsndfile
         if: startsWith(matrix.os, 'ubuntu')
         run: |

From efcc57486c51c1b65c7adfff292f75477f49e75c Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 19 Nov 2024 09:20:42 +0100
Subject: [PATCH 17/56] Remove 3.13 (and add 3.9) for now

---
 .github/workflows/run-tests.yml | 2 +-
 pyproject.toml                  | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index b8e47eb5..8074617e 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - name: Setup uv
diff --git a/pyproject.toml b/pyproject.toml
index 96aaf5a6..14080e5c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,10 +8,10 @@ description = "The WFDB Python package: tools for reading, writing, and processi
 authors = [{name = "The Laboratory for Computational Physiology", email = "contact@physionet.org"}]
 license = {text = "MIT License"}
 readme = "README.md"
-requires-python = ">= 3.10"
+requires-python = ">= 3.9"
 dependencies = [
     "numpy >= 1.26.4",
-    "scipy >= 1.14.0",
+    "scipy >= 1.13.0",
     "pandas >= 2.2.0",
     "soundfile >= 0.10.0",
     "matplotlib >= 3.2.2",
@@ -35,7 +35,7 @@ documentation = "https://wfdb.readthedocs.io/"
 
 [tool.black]
 line-length = 80
-target-version = ["py310"]
+target-version = ["py39"]
 
 [tool.hatch.build.targets.sdist]
 exclude = [

From a9366ecf30617609626b086a87a940f934d38ec6 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 19 Nov 2024 10:45:33 +0100
Subject: [PATCH 18/56] Force numpy >= 2.0.0

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 14080e5c..b4bda8e5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,7 +10,7 @@ license = {text = "MIT License"}
 readme = "README.md"
 requires-python = ">= 3.9"
 dependencies = [
-    "numpy >= 1.26.4",
+    "numpy >= 2.0.0",
     "scipy >= 1.13.0",
     "pandas >= 2.2.0",
     "soundfile >= 0.10.0",

From 0556a678ed55d63a422d9125db0acd2679bdaff3 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 09:42:10 +0100
Subject: [PATCH 19/56] Revert to numpy >= 1.26.4

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b4bda8e5..14080e5c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,7 +10,7 @@ license = {text = "MIT License"}
 readme = "README.md"
 requires-python = ">= 3.9"
 dependencies = [
-    "numpy >= 2.0.0",
+    "numpy >= 1.26.4",
     "scipy >= 1.13.0",
     "pandas >= 2.2.0",
     "soundfile >= 0.10.0",

From 9825b4a2a56b3090611d58086ca4f1e374c86847 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 09:45:11 +0100
Subject: [PATCH 20/56] Use uv pip

---
 .github/workflows/run-tests.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index 8074617e..cbb56971 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -28,11 +28,14 @@ jobs:
         run: |
           sudo apt-get install -y libsndfile1
       - name: Install dependencies
-        run: uv sync --all-extras
+        run: |
+          uv venv
+          source .venv/bin/activate
+          uv pip install ".[dev]"
       - name: Run tests
-        run: uv run pytest
+        run: pytest
       - name: Check source code format
-        run: uv run black --check --diff .
+        run: black --check --diff .
 
   test-deb10-i386:
     runs-on: ubuntu-latest

From c1a4dae94bfc315183136b8ed00bd14f3203b9c1 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 09:46:53 +0100
Subject: [PATCH 21/56] Activate venv

---
 .github/workflows/run-tests.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index cbb56971..026e2ef0 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -30,10 +30,11 @@ jobs:
       - name: Install dependencies
         run: |
           uv venv
-          source .venv/bin/activate
           uv pip install ".[dev]"
       - name: Run tests
-        run: pytest
+        run: |
+          source .venv/bin/activate
+          pytest
       - name: Check source code format
         run: black --check --diff .
 

From e0ade6a599c2263784ad361cf22f324a58d9b0fb Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 09:57:17 +0100
Subject: [PATCH 22/56] Use system Python

---
 .github/workflows/run-tests.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index 026e2ef0..230ea067 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -10,6 +10,9 @@ on:
     branches:
       - main
 
+env:
+  UV_SYSTEM_PYTHON: 1
+
 jobs:
   build:
     runs-on: ${{ matrix.os }}
@@ -29,11 +32,9 @@ jobs:
           sudo apt-get install -y libsndfile1
       - name: Install dependencies
         run: |
-          uv venv
           uv pip install ".[dev]"
       - name: Run tests
         run: |
-          source .venv/bin/activate
           pytest
       - name: Check source code format
         run: black --check --diff .

From 37df1e7713fe59ccf29ca262ebe389d63694f1ab Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 10:14:05 +0100
Subject: [PATCH 23/56] Use setup-python

---
 .github/workflows/run-tests.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index 230ea067..97f1af20 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -22,10 +22,12 @@ jobs:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
-      - name: Setup uv
+      - name: Install uv
         uses: astral-sh/setup-uv@v3
-      - name: Install Python ${{ matrix.python-version }}
-        run: uv python install ${{ matrix.python-version }}
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
       - name: Install libsndfile
         if: startsWith(matrix.os, 'ubuntu')
         run: |

From 18edd50d99dead87b98a3b6b386ebb650a0ff02a Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 10:17:25 +0100
Subject: [PATCH 24/56] Ping

---
 .github/workflows/run-tests.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index 97f1af20..26db8428 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -1,6 +1,3 @@
-# Link repository with GitHub Actions
-# https://docs.github.com/en/actions/learn-github-actions/introduction-to-github-actions
-
 name: run-tests
 on:
   push:

From 4e81718b86d734fa496d71a2776f84ccc5ff12e0 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 10:37:39 +0100
Subject: [PATCH 25/56] Add 3.13

---
 .github/workflows/run-tests.yml | 23 ++++++++---------------
 1 file changed, 8 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index 26db8428..a6d2aca9 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -11,18 +11,16 @@ env:
   UV_SYSTEM_PYTHON: 1
 
 jobs:
-  build:
+  test:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
-      - name: Install uv
-        uses: astral-sh/setup-uv@v3
-      - name: Install Python
-        uses: actions/setup-python@v5
+      - uses: astral-sh/setup-uv@v3
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install libsndfile
@@ -30,12 +28,10 @@ jobs:
         run: |
           sudo apt-get install -y libsndfile1
       - name: Install dependencies
-        run: |
-          uv pip install ".[dev]"
+        run: uv pip install ".[dev]"
       - name: Run tests
-        run: |
-          pytest
-      - name: Check source code format
+        run: pytest
+      - name: Check style
         run: black --check --diff .
 
   test-deb10-i386:
@@ -54,16 +50,13 @@ jobs:
                   python3-soundfile \
                   python3-pytest \
                   git
-
       # Note: "actions/checkout@v2" requires libstdc++6:amd64 to be
       # installed in the container.  To keep things simple, use
       # "actions/checkout@v1" instead.
       # https://github.com/actions/checkout/issues/334
       - uses: actions/checkout@v1
-
       - name: Run tests
-        run: |
-          pytest-3
+        run: pytest-3
 
   build-documentation:
     runs-on: ubuntu-20.04

From 16071e4c74218edcbde0c18055feb6546f583501 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 10:51:17 +0100
Subject: [PATCH 26/56] Split jobs

---
 .github/workflows/docs.yml                    | 23 +++++++++++++++++++
 .github/workflows/{run-tests.yml => test.yml} | 18 +++------------
 2 files changed, 26 insertions(+), 15 deletions(-)
 create mode 100644 .github/workflows/docs.yml
 rename .github/workflows/{run-tests.yml => test.yml} (82%)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
new file mode 100644
index 00000000..e47e6625
--- /dev/null
+++ b/.github/workflows/docs.yml
@@ -0,0 +1,23 @@
+name: Build docs
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build-documentation:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r docs/requirements.txt
+      - name: Build documentation
+        run: |
+          cd docs
+          make html
\ No newline at end of file
diff --git a/.github/workflows/run-tests.yml b/.github/workflows/test.yml
similarity index 82%
rename from .github/workflows/run-tests.yml
rename to .github/workflows/test.yml
index a6d2aca9..8fc24140 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/test.yml
@@ -1,4 +1,5 @@
-name: run-tests
+name: Test
+
 on:
   push:
     branches:
@@ -12,11 +13,11 @@ env:
 
 jobs:
   test:
-    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+    runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
       - uses: astral-sh/setup-uv@v3
@@ -57,16 +58,3 @@ jobs:
       - uses: actions/checkout@v1
       - name: Run tests
         run: pytest-3
-
-  build-documentation:
-    runs-on: ubuntu-20.04
-    steps:
-      - uses: actions/checkout@v3
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r docs/requirements.txt
-      - name: Build documentation
-        run: |
-          cd docs
-          make html

From dfdd451a6b78d64735f5b31a9c9cfc7dea953281 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:03:34 +0100
Subject: [PATCH 27/56] Rename

---
 .github/workflows/docs.yml | 6 +++---
 .github/workflows/test.yml | 3 +++
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index e47e6625..3dcbd965 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -1,4 +1,4 @@
-name: Build docs
+name: Build
 
 on:
   push:
@@ -9,7 +9,7 @@ on:
       - main
 
 jobs:
-  build-documentation:
+  docs:
     runs-on: ubuntu-20.04
     steps:
       - uses: actions/checkout@v3
@@ -20,4 +20,4 @@ jobs:
       - name: Build documentation
         run: |
           cd docs
-          make html
\ No newline at end of file
+          make html
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 8fc24140..585ab5a3 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,6 +13,7 @@ env:
 
 jobs:
   test:
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with {{ matrix.numpy }}
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]
@@ -36,6 +37,7 @@ jobs:
         run: black --check --diff .
 
   test-deb10-i386:
+    name: Python 3.9 on Debian 10 i386
     runs-on: ubuntu-latest
     container: i386/debian:10
     steps:
@@ -51,6 +53,7 @@ jobs:
                   python3-soundfile \
                   python3-pytest \
                   git
+          python3 --version
       # Note: "actions/checkout@v2" requires libstdc++6:amd64 to be
       # installed in the container.  To keep things simple, use
       # "actions/checkout@v1" instead.

From 510e45faa59a8769916a04d80606e59ac9e00c47 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:04:31 +0100
Subject: [PATCH 28/56] Remove numpy matrix

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 585ab5a3..601ac7ec 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,7 +13,7 @@ env:
 
 jobs:
   test:
-    name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with {{ matrix.numpy }}
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]

From a7e7ed7f8474b3df2425503330f7470d53a9b721 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:05:14 +0100
Subject: [PATCH 29/56] Fix name for Debian test

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 601ac7ec..6a8d8fc3 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -37,7 +37,7 @@ jobs:
         run: black --check --diff .
 
   test-deb10-i386:
-    name: Python 3.9 on Debian 10 i386
+    name: Python 3.7 on Debian 10 i386
     runs-on: ubuntu-latest
     container: i386/debian:10
     steps:

From 3f43fd2ec8c6b36161b948feb67c0a12825e7b3f Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:08:12 +0100
Subject: [PATCH 30/56] Downgrade pandas

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 14080e5c..5e99c301 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,7 @@ requires-python = ">= 3.9"
 dependencies = [
     "numpy >= 1.26.4",
     "scipy >= 1.13.0",
-    "pandas >= 2.2.0",
+    "pandas >= 2.1.0",
     "soundfile >= 0.10.0",
     "matplotlib >= 3.2.2",
     "requests >= 2.8.1",

From 2ea3f8fc7cb8a52ea25babded26d6ce3e6b7a25c Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:12:53 +0100
Subject: [PATCH 31/56] Revert pandas

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5e99c301..f550ebd7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,7 @@ requires-python = ">= 3.9"
 dependencies = [
     "numpy >= 1.26.4",
     "scipy >= 1.13.0",
-    "pandas >= 2.1.0",
+    "pandas >= 2.2.3",
     "soundfile >= 0.10.0",
     "matplotlib >= 3.2.2",
     "requests >= 2.8.1",

From fc91a13c82fa5e77880687c596127bd08a26d490 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:15:44 +0100
Subject: [PATCH 32/56] Numpy matrix

---
 .github/workflows/test.yml | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 6a8d8fc3..4d7bd204 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,11 +13,21 @@ env:
 
 jobs:
   test:
-    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with {{ matrix.numpy }}
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        numpy: ["numpy"]
+        include:
+          - python-version: "3.9"
+            numpy: "numpy==1.26.4"
+          - python-version: "3.10"
+            numpy: "numpy==1.26.4"
+          - python-version: "3.11"
+            numpy: "numpy==1.26.4"
+          - python-version: "3.12"
+            numpy: "numpy==1.26.4"
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
@@ -30,7 +40,9 @@ jobs:
         run: |
           sudo apt-get install -y libsndfile1
       - name: Install dependencies
-        run: uv pip install ".[dev]"
+        run: |
+          uv pip install ".[dev]"
+          uv pip install ${{ matrix.numpy }}
       - name: Run tests
         run: pytest
       - name: Check style

From c773875c044983a35236f57e4a35e6caf11abec3 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:17:26 +0100
Subject: [PATCH 33/56] Fix matrix

---
 .github/workflows/test.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4d7bd204..241bc06f 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -21,13 +21,13 @@ jobs:
         numpy: ["numpy"]
         include:
           - python-version: "3.9"
-            numpy: "numpy==1.26.4"
+            numpy: numpy==1.26.4
           - python-version: "3.10"
-            numpy: "numpy==1.26.4"
+            numpy: numpy==1.26.4
           - python-version: "3.11"
-            numpy: "numpy==1.26.4"
+            numpy: numpy==1.26.4
           - python-version: "3.12"
-            numpy: "numpy==1.26.4"
+            numpy: numpy==1.26.4
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4

From fb7120ea85dd10131d951def087e414e2ce37878 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:20:16 +0100
Subject: [PATCH 34/56] Temporarily remove Debian

---
 .github/workflows/test.yml | 58 +++++++++++++++++++-------------------
 1 file changed, 29 insertions(+), 29 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 241bc06f..af294b22 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -21,13 +21,13 @@ jobs:
         numpy: ["numpy"]
         include:
           - python-version: "3.9"
-            numpy: numpy==1.26.4
+            numpy: "numpy==1.26.4"
           - python-version: "3.10"
-            numpy: numpy==1.26.4
+            numpy: "numpy==1.26.4"
           - python-version: "3.11"
-            numpy: numpy==1.26.4
+            numpy: "numpy==1.26.4"
           - python-version: "3.12"
-            numpy: numpy==1.26.4
+            numpy: "numpy==1.26.4"
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
@@ -48,28 +48,28 @@ jobs:
       - name: Check style
         run: black --check --diff .
 
-  test-deb10-i386:
-    name: Python 3.7 on Debian 10 i386
-    runs-on: ubuntu-latest
-    container: i386/debian:10
-    steps:
-      - name: Install dependencies
-        run: |
-          apt-get update
-          apt-get install -y --no-install-recommends \
-                  python3-matplotlib \
-                  python3-numpy \
-                  python3-pandas \
-                  python3-requests \
-                  python3-scipy \
-                  python3-soundfile \
-                  python3-pytest \
-                  git
-          python3 --version
-      # Note: "actions/checkout@v2" requires libstdc++6:amd64 to be
-      # installed in the container.  To keep things simple, use
-      # "actions/checkout@v1" instead.
-      # https://github.com/actions/checkout/issues/334
-      - uses: actions/checkout@v1
-      - name: Run tests
-        run: pytest-3
+  # test-deb10-i386:
+  #   name: Python 3.7 on Debian 10 i386
+  #   runs-on: ubuntu-latest
+  #   container: i386/debian:10
+  #   steps:
+  #     - name: Install dependencies
+  #       run: |
+  #         apt-get update
+  #         apt-get install -y --no-install-recommends \
+  #                 python3-matplotlib \
+  #                 python3-numpy \
+  #                 python3-pandas \
+  #                 python3-requests \
+  #                 python3-scipy \
+  #                 python3-soundfile \
+  #                 python3-pytest \
+  #                 git
+  #         python3 --version
+  #     # Note: "actions/checkout@v2" requires libstdc++6:amd64 to be
+  #     # installed in the container.  To keep things simple, use
+  #     # "actions/checkout@v1" instead.
+  #     # https://github.com/actions/checkout/issues/334
+  #     - uses: actions/checkout@v1
+  #     - name: Run tests
+  #       run: pytest-3

From 6fd6bc0bd609dca0c28037d55951fe808025187f Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:27:03 +0100
Subject: [PATCH 35/56] Re-enable

---
 .github/workflows/test.yml | 50 +++++++++++++++++++-------------------
 1 file changed, 25 insertions(+), 25 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index af294b22..4d7bd204 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -48,28 +48,28 @@ jobs:
       - name: Check style
         run: black --check --diff .
 
-  # test-deb10-i386:
-  #   name: Python 3.7 on Debian 10 i386
-  #   runs-on: ubuntu-latest
-  #   container: i386/debian:10
-  #   steps:
-  #     - name: Install dependencies
-  #       run: |
-  #         apt-get update
-  #         apt-get install -y --no-install-recommends \
-  #                 python3-matplotlib \
-  #                 python3-numpy \
-  #                 python3-pandas \
-  #                 python3-requests \
-  #                 python3-scipy \
-  #                 python3-soundfile \
-  #                 python3-pytest \
-  #                 git
-  #         python3 --version
-  #     # Note: "actions/checkout@v2" requires libstdc++6:amd64 to be
-  #     # installed in the container.  To keep things simple, use
-  #     # "actions/checkout@v1" instead.
-  #     # https://github.com/actions/checkout/issues/334
-  #     - uses: actions/checkout@v1
-  #     - name: Run tests
-  #       run: pytest-3
+  test-deb10-i386:
+    name: Python 3.7 on Debian 10 i386
+    runs-on: ubuntu-latest
+    container: i386/debian:10
+    steps:
+      - name: Install dependencies
+        run: |
+          apt-get update
+          apt-get install -y --no-install-recommends \
+                  python3-matplotlib \
+                  python3-numpy \
+                  python3-pandas \
+                  python3-requests \
+                  python3-scipy \
+                  python3-soundfile \
+                  python3-pytest \
+                  git
+          python3 --version
+      # Note: "actions/checkout@v2" requires libstdc++6:amd64 to be
+      # installed in the container.  To keep things simple, use
+      # "actions/checkout@v1" instead.
+      # https://github.com/actions/checkout/issues/334
+      - uses: actions/checkout@v1
+      - name: Run tests
+        run: pytest-3

From 8357620c9214c3b3f34a75fb700abf2409c3517a Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:28:54 +0100
Subject: [PATCH 36/56] Test single OS

---
 .github/workflows/test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4d7bd204..c98cfa5e 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -16,7 +16,7 @@ jobs:
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with {{ matrix.numpy }}
     strategy:
       matrix:
-        os: [windows-latest, ubuntu-latest, macos-latest]
+        #os: [windows-latest, ubuntu-latest, macos-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
         numpy: ["numpy"]
         include:
@@ -28,7 +28,7 @@ jobs:
             numpy: "numpy==1.26.4"
           - python-version: "3.12"
             numpy: "numpy==1.26.4"
-    runs-on: ${{ matrix.os }}
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - uses: astral-sh/setup-uv@v3

From 386a462b32863292c2846cd5b6c63e13e4fee99e Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:29:33 +0100
Subject: [PATCH 37/56] Fix name

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index c98cfa5e..88350688 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,7 +13,7 @@ env:
 
 jobs:
   test:
-    name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with {{ matrix.numpy }}
+    name: Python ${{ matrix.python-version }} with {{ matrix.numpy }}
     strategy:
       matrix:
         #os: [windows-latest, ubuntu-latest, macos-latest]

From d6df0ce9aa323a1dd79606382a228d35e8fe34bd Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:30:12 +0100
Subject: [PATCH 38/56] Remove quotes

---
 .github/workflows/test.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 88350688..0d0d1cc1 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -21,13 +21,13 @@ jobs:
         numpy: ["numpy"]
         include:
           - python-version: "3.9"
-            numpy: "numpy==1.26.4"
+            numpy: numpy==1.26.4
           - python-version: "3.10"
-            numpy: "numpy==1.26.4"
+            numpy: numpy==1.26.4
           - python-version: "3.11"
-            numpy: "numpy==1.26.4"
+            numpy: numpy==1.26.4
           - python-version: "3.12"
-            numpy: "numpy==1.26.4"
+            numpy: numpy==1.26.4
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

From ae8ebe46e0acb644f4679be7822cad0e8e96353f Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:31:36 +0100
Subject: [PATCH 39/56] Forgot $

---
 .github/workflows/test.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 0d0d1cc1..316ec9fe 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,7 +13,7 @@ env:
 
 jobs:
   test:
-    name: Python ${{ matrix.python-version }} with {{ matrix.numpy }}
+    name: Python ${{ matrix.python-version }} with ${{ matrix.numpy }}
     strategy:
       matrix:
         #os: [windows-latest, ubuntu-latest, macos-latest]
@@ -21,13 +21,13 @@ jobs:
         numpy: ["numpy"]
         include:
           - python-version: "3.9"
-            numpy: numpy==1.26.4
+            numpy: "numpy==1.26.4"
           - python-version: "3.10"
-            numpy: numpy==1.26.4
+            numpy: "numpy==1.26.4"
           - python-version: "3.11"
-            numpy: numpy==1.26.4
+            numpy: "numpy==1.26.4"
           - python-version: "3.12"
-            numpy: numpy==1.26.4
+            numpy: "numpy==1.26.4"
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

From fb5d6ada20f043cbf680e178a6bb3cc5b288ed45 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:32:01 +0100
Subject: [PATCH 40/56] Try single command

---
 .github/workflows/test.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 316ec9fe..f728cee2 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -41,8 +41,7 @@ jobs:
           sudo apt-get install -y libsndfile1
       - name: Install dependencies
         run: |
-          uv pip install ".[dev]"
-          uv pip install ${{ matrix.numpy }}
+          uv pip install ".[dev]" ${{ matrix.numpy }}
       - name: Run tests
         run: pytest
       - name: Check style

From 39f3a987dd02543675cd603e1f5091d203f96a17 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:37:48 +0100
Subject: [PATCH 41/56] Simplify matrix

---
 .github/workflows/test.yml | 18 +++++++-----------
 1 file changed, 7 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index f728cee2..93fc65b6 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -16,19 +16,15 @@ jobs:
     name: Python ${{ matrix.python-version }} with ${{ matrix.numpy }}
     strategy:
       matrix:
-        #os: [windows-latest, ubuntu-latest, macos-latest]
+        os: [windows-latest, ubuntu-latest, macos-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
-        numpy: ["numpy"]
-        include:
-          - python-version: "3.9"
+        numpy:
+          - "numpy"
+          - "numpy==1.26.4"
+        exclude:
+          - python-version: "3.13"
             numpy: "numpy==1.26.4"
-          - python-version: "3.10"
-            numpy: "numpy==1.26.4"
-          - python-version: "3.11"
-            numpy: "numpy==1.26.4"
-          - python-version: "3.12"
-            numpy: "numpy==1.26.4"
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
       - uses: astral-sh/setup-uv@v3

From 9e234ea769ac045038047da376c2a08d334319c9 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:39:31 +0100
Subject: [PATCH 42/56] Add OS name

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 93fc65b6..79247518 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,7 +13,7 @@ env:
 
 jobs:
   test:
-    name: Python ${{ matrix.python-version }} with ${{ matrix.numpy }}
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with ${{ matrix.numpy }}
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]

From 781690d2a4663040d3ddc4a5466cffd266082b41 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:41:52 +0100
Subject: [PATCH 43/56] Improve name

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 79247518..5fb238de 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,7 +13,7 @@ env:
 
 jobs:
   test:
-    name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with ${{ matrix.numpy }}
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}${{ matrix.numpy != 'numpy' ? ' with ' + matrix.numpy : '' }}
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]

From f804e789fa89052760d75b2cc5964a5315de7962 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:43:23 +0100
Subject: [PATCH 44/56] Revert

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 5fb238de..79247518 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,7 +13,7 @@ env:
 
 jobs:
   test:
-    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}${{ matrix.numpy != 'numpy' ? ' with ' + matrix.numpy : '' }}
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with ${{ matrix.numpy }}
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]

From 1f91640b57f1843f97e5755a6aebaea0f63e1a3a Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:44:03 +0100
Subject: [PATCH 45/56] Try another variant

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 79247518..6b9ed977 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,7 +13,7 @@ env:
 
 jobs:
   test:
-    name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with ${{ matrix.numpy }}
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}${{ matrix.numpy != 'numpy' && ' with ' + matrix.numpy || '' }}
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]

From fc4db5013dcde63dd41c107884c6e90726d9e4b5 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 11:44:47 +0100
Subject: [PATCH 46/56] OK forget it

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 6b9ed977..79247518 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,7 +13,7 @@ env:
 
 jobs:
   test:
-    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}${{ matrix.numpy != 'numpy' && ' with ' + matrix.numpy || '' }}
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with ${{ matrix.numpy }}
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]

From 9ee80270f36d0b3edabc78758b4f53295594d025 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 12:08:57 +0100
Subject: [PATCH 47/56] Only test NumPy 1.26.4 on Python 3.9

---
 .github/workflows/test.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 79247518..5303efcf 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -18,11 +18,9 @@ jobs:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
-        numpy:
-          - "numpy"
-          - "numpy==1.26.4"
-        exclude:
-          - python-version: "3.13"
+        numpy: ["numpy"]
+        include:
+          - python-version: "3.9"
             numpy: "numpy==1.26.4"
     runs-on: ${{ matrix.os }}
     steps:

From e82bfac97b5f2ec52e4d073df5298fbb42e12028 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 12:20:02 +0100
Subject: [PATCH 48/56] Try with condition

---
 .github/workflows/test.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 5303efcf..a4147509 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,14 +13,14 @@ env:
 
 jobs:
   test:
-    name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with ${{ matrix.numpy }}
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
-        numpy: ["numpy"]
         include:
-          - python-version: "3.9"
+          - os: ubuntu-latest
+            python-version: "3.9"
             numpy: "numpy==1.26.4"
     runs-on: ${{ matrix.os }}
     steps:
@@ -35,7 +35,9 @@ jobs:
           sudo apt-get install -y libsndfile1
       - name: Install dependencies
         run: |
-          uv pip install ".[dev]" ${{ matrix.numpy }}
+          uv pip install ".[dev]" 
+      - if: ${{ matrix.numpy }}
+        run: uv pip install ${{ matrix.numpy }}
       - name: Run tests
         run: pytest
       - name: Check style

From ad26811b639b60f697831d1a3cd8b62828254d5d Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 12:24:31 +0100
Subject: [PATCH 49/56] Use weak_and_warn

---
 .github/workflows/test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a4147509..36b23ec0 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -10,6 +10,7 @@ on:
 
 env:
   UV_SYSTEM_PYTHON: 1
+  NPY_PROMOTION_STATE: weak_and_warn
 
 jobs:
   test:

From 2387ca3ed3b661de777035826e86a86404b17ad2 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 12:35:16 +0100
Subject: [PATCH 50/56] Don't fail fast

---
 .github/workflows/test.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 36b23ec0..ce6493c4 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -12,6 +12,8 @@ env:
   UV_SYSTEM_PYTHON: 1
   NPY_PROMOTION_STATE: weak_and_warn
 
+jobs.test.strategy.fail-fast: false
+
 jobs:
   test:
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }}

From 537cc7a1f0f8fdd8ab6ebb5613f9266b426ad13d Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 12:37:21 +0100
Subject: [PATCH 51/56] Fix syntax

---
 .github/workflows/test.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ce6493c4..48bc2e63 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -12,12 +12,11 @@ env:
   UV_SYSTEM_PYTHON: 1
   NPY_PROMOTION_STATE: weak_and_warn
 
-jobs.test.strategy.fail-fast: false
-
 jobs:
   test:
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]

From 235f215232851139390d66671c1f34e7c27988cc Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 12:47:09 +0100
Subject: [PATCH 52/56] Fix invalid escape sequence

---
 wfdb/processing/peaks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wfdb/processing/peaks.py b/wfdb/processing/peaks.py
index dd276950..47d7ce48 100644
--- a/wfdb/processing/peaks.py
+++ b/wfdb/processing/peaks.py
@@ -4,7 +4,7 @@
 
 
 def find_peaks(sig):
-    """
+    r"""
     Find hard peaks and soft peaks in a signal, defined as follows:
 
     - Hard peak: a peak that is either /\ or \/.

From 68d5c04d5ebb2b5415d87bd647de6e29a38aeca7 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 12:55:46 +0100
Subject: [PATCH 53/56] Fix dtype promotion warning

---
 wfdb/io/convert/edf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wfdb/io/convert/edf.py b/wfdb/io/convert/edf.py
index e3096884..ef8142b2 100644
--- a/wfdb/io/convert/edf.py
+++ b/wfdb/io/convert/edf.py
@@ -399,7 +399,7 @@ def read_edf(
         }
 
     sig_data = np.empty((sig_len, n_sig))
-    temp_sig_data = np.fromfile(edf_file, dtype=np.int16)
+    temp_sig_data = np.fromfile(edf_file, dtype=np.int64)
     temp_sig_data = temp_sig_data.reshape((-1, sum(samps_per_block)))
     temp_all_sigs = np.hsplit(temp_sig_data, np.cumsum(samps_per_block)[:-1])
     for i in range(n_sig):

From afbf5420301e9ad63efc09b4a5742469eab34ef9 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 13:01:41 +0100
Subject: [PATCH 54/56] Try again

---
 wfdb/io/convert/edf.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/wfdb/io/convert/edf.py b/wfdb/io/convert/edf.py
index ef8142b2..ef5ea947 100644
--- a/wfdb/io/convert/edf.py
+++ b/wfdb/io/convert/edf.py
@@ -399,25 +399,27 @@ def read_edf(
         }
 
     sig_data = np.empty((sig_len, n_sig))
-    temp_sig_data = np.fromfile(edf_file, dtype=np.int64)
+    temp_sig_data = np.fromfile(edf_file, dtype=np.int16)
     temp_sig_data = temp_sig_data.reshape((-1, sum(samps_per_block)))
     temp_all_sigs = np.hsplit(temp_sig_data, np.cumsum(samps_per_block)[:-1])
     for i in range(n_sig):
         # Check if `samps_per_frame` has all equal values
         if samps_per_frame.count(samps_per_frame[0]) == len(samps_per_frame):
             sig_data[:, i] = (
-                temp_all_sigs[i].flatten() - baseline[i]
+                temp_all_sigs[i].flatten().astype("int64") - baseline[i]
             ) / adc_gain_all[i]
         else:
             temp_sig_data = temp_all_sigs[i].flatten()
             if samps_per_frame[i] == 1:
-                sig_data[:, i] = (temp_sig_data - baseline[i]) / adc_gain_all[i]
+                sig_data[:, i] = (
+                    temp_sig_data.astype("int64") - baseline[i]
+                ) / adc_gain_all[i]
             else:
                 for j in range(sig_len):
                     start_ind = j * samps_per_frame[i]
                     stop_ind = start_ind + samps_per_frame[i]
                     sig_data[j, i] = np.mean(
-                        (temp_sig_data[start_ind:stop_ind] - baseline[i])
+                        (temp_sig_data[start_ind:stop_ind].astype("int64") - baseline[i])
                         / adc_gain_all[i]
                     )
 

From 1a437e65f5a2f509180bfae1fe9d266ad6523509 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 13:03:09 +0100
Subject: [PATCH 55/56] Maybe better

---
 wfdb/io/convert/edf.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/wfdb/io/convert/edf.py b/wfdb/io/convert/edf.py
index ef5ea947..27bd5669 100644
--- a/wfdb/io/convert/edf.py
+++ b/wfdb/io/convert/edf.py
@@ -399,27 +399,27 @@ def read_edf(
         }
 
     sig_data = np.empty((sig_len, n_sig))
-    temp_sig_data = np.fromfile(edf_file, dtype=np.int16)
+    temp_sig_data = np.fromfile(edf_file, dtype=np.int16).astype("int64")
     temp_sig_data = temp_sig_data.reshape((-1, sum(samps_per_block)))
     temp_all_sigs = np.hsplit(temp_sig_data, np.cumsum(samps_per_block)[:-1])
     for i in range(n_sig):
         # Check if `samps_per_frame` has all equal values
         if samps_per_frame.count(samps_per_frame[0]) == len(samps_per_frame):
             sig_data[:, i] = (
-                temp_all_sigs[i].flatten().astype("int64") - baseline[i]
+                temp_all_sigs[i].flatten() - baseline[i]
             ) / adc_gain_all[i]
         else:
             temp_sig_data = temp_all_sigs[i].flatten()
             if samps_per_frame[i] == 1:
                 sig_data[:, i] = (
-                    temp_sig_data.astype("int64") - baseline[i]
+                    temp_sig_data - baseline[i]
                 ) / adc_gain_all[i]
             else:
                 for j in range(sig_len):
                     start_ind = j * samps_per_frame[i]
                     stop_ind = start_ind + samps_per_frame[i]
                     sig_data[j, i] = np.mean(
-                        (temp_sig_data[start_ind:stop_ind].astype("int64") - baseline[i])
+                        (temp_sig_data[start_ind:stop_ind] - baseline[i])
                         / adc_gain_all[i]
                     )
 

From 0269bf7614c712480f7e59da753a276ba5720351 Mon Sep 17 00:00:00 2001
From: Clemens Brunner <clemens.brunner@gmail.com>
Date: Tue, 26 Nov 2024 13:08:42 +0100
Subject: [PATCH 56/56] Fix style

---
 wfdb/io/convert/edf.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/wfdb/io/convert/edf.py b/wfdb/io/convert/edf.py
index 27bd5669..32a3b193 100644
--- a/wfdb/io/convert/edf.py
+++ b/wfdb/io/convert/edf.py
@@ -411,9 +411,7 @@ def read_edf(
         else:
             temp_sig_data = temp_all_sigs[i].flatten()
             if samps_per_frame[i] == 1:
-                sig_data[:, i] = (
-                    temp_sig_data - baseline[i]
-                ) / adc_gain_all[i]
+                sig_data[:, i] = (temp_sig_data - baseline[i]) / adc_gain_all[i]
             else:
                 for j in range(sig_len):
                     start_ind = j * samps_per_frame[i]